Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
Nicole T. Perna,Guy Plunkett,Valerie Burland,Bob Mau,Jeremy D. Glasner,Debra J. Rose,George F. Mayhew,Peter Evans,Jason Gregor,Heather A. Kirkpatrick,György Pósfai,Jeremiah D. Hackett,Sara A. Klink,Adam T. Boutin,Ying Shao,Leslie Miller,Erik J. Grotbeck,N. Wayne Davis,Alex Lim,Eileen T. Dimalanta,Konstantinos Potamousis,Jennifer Apodaca,Thomas Anantharaman,Jieyi Lin,Galex Yen,David C. Schwartz,Rodney A. Welch,Frederick R. Blattner +27 more
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TLDR
It is found that lateral gene transfer is far more extensive than previously anticipated and 1,387 new genes encoded in strain-specific clusters of diverse sizes were found in O157:H7, including candidate virulence factors, alternative metabolic capacities, several prophages and other new functions—all of which could be targets for surveillance.Abstract:
The bacterium Escherichia coli O157:H7 is a worldwide threat to public health and has been implicated in many outbreaks of haemorrhagic colitis, some of which included fatalities caused by haemolytic uraemic syndrome. Close to 75,000 cases of O157:H7 infection are now estimated to occur annually in the United States. The severity of disease, the lack of effective treatment and the potential for large-scale outbreaks from contaminated food supplies have propelled intensive research on the pathogenesis and detection of E. coli O157:H7 (ref. 4). Here we have sequenced the genome of E. coli O157:H7 to identify candidate genes responsible for pathogenesis, to develop better methods of strain detection and to advance our understanding of the evolution of E. coli, through comparison with the genome of the non-pathogenic laboratory strain E. coli K-12 (ref. 5). We find that lateral gene transfer is far more extensive than previously anticipated. In fact, 1,387 new genes encoded in strain-specific clusters of diverse sizes were found in O157:H7. These include candidate virulence factors, alternative metabolic capacities, several prophages and other new functions--all of which could be targets for surveillance.read more
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Pathogenic Escherichia coli
TL;DR: Few microorganisms are as versatile as Escherichia coli; it can also be a highly versatile, and frequently deadly, pathogen.
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Mauve: multiple alignment of conserved genomic sequence with rearrangements.
TL;DR: This work presents methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer and evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.
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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
TL;DR: A new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss is described, demonstrating high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental loss and loss.
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BLAST Ring Image Generator (BRIG) : simple prokaryote genome comparisons
TL;DR: BRIG is a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface and will perform all required file parsing and BLAST comparisons automatically.
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Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
Michael McClelland,Kenneth E. Sanderson,John Spieth,Sandra W. Clifton,Phil Latreille,Laura Courtney,Steffen Porwollik,Johar Ali,Mike Dante,Feiyu Du,Shunfang Hou,Dan Layman,Shawn Leonard,Christine Nguyen,Kelsi Scott,Andrea Holmes,Neenu Grewal,Elizabeth Mulvaney,Ellen E. Ryan,Hui Sun,Liliana Florea,Liliana Florea,Webb Miller,Tamberlyn Stoneking,Michael Nhan,Robert H. Waterston,Richard K. Wilson +26 more
TL;DR: The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A and Klebsiella pneumoniae as mentioned in this paper.
References
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Journal ArticleDOI
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